Laboratory for Cell Dynamics Research | RIKEN BDR

Laboratory for Cell Dynamics Research

Team Leader

Toshio YanagidaPh.D.
(Apr. 2018 ~ Mar. 2020)

Eisuke NishidaPh.D.
(Apr. 2020 ~ Mar. 2021)

Photo of principal investigator

    [Closed Mar. 2021]

Clarifying the mystery of life through control of biomolecular assembly and super-resolution imaging

Research Summary

We have been focusing on the development of single-molecule imaging and nano-scale manipulation techniques and their application to the study of biological molecular motors. One of our most important insights on how these motors operate is that they do not filter Brownian noise, instead using this noise to perform robustly. These same techniques have afforded us new understanding on how information is passed intracellularly and how the brain maps a visual stimulus. Noise that is exploited and not filtered we call “yuragi”. Yuragi is exclusive to living organisms, enabling more flexibility and less energy demands for their function. Currently, by collaborating with robotics engineers and information scientists, we are investigating ways to use yuragi in complex information networks such as robots and the internet. By studying yuragi in biological systems and successfully applying yuragi to artificial systems, a better understanding of how biological systems respond efficiently to environmental changes should emerge.

Research Theme

  • Mechano Biology
  • Systems biophysics of heart
  • Super-resolution imaging
  • Variability of genomic structure

Main Publications List

  • Fujita K, Ohmachi M, Ikezaki K, et al.
    Direct visualization of human myosin II force generation using DNA origami-based thick filaments.
    Communications Biology 2, 437 (2019). doi: 10.1038/s42003-019-0683-0
  • Fujita K, Iwaki M, Yanagida T.
    Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA.
    Nature Communications 7. 13788 (2016) doi :10.1038/ncomms13788
  • Iwaki M, Wickham SF, Ikezaki K, et al.
    A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads.
    Nature Communications 7. 13715 (2016) doi :10.1038/ncomms13715
  • Iwaki M, Iwane AH, Ikezaki K, Yanagida T.
    Local Heat Activation of Single Myosins Based on Optical Trapping of Gold Nanoparticles.
    Nano Letters 15(4). 2456-2461 (2015) doi :10.1021/nl5049059
  • Karagiannis P, Ishii Y, Yanagida T.
    Molecular Machines Like Myosin Use Randomness to Behave Predictably.
    Chemical Reviews 114(6). 3318-3334 (2014) doi :10.1021/cr400344n
  • Fujita K, Iwaki M, Iwane AH, et al.
    Switching of myosin-V motion between the lever-arm swing and Brownian search-and-catch.
    Nature Communications 3. 956 (2012) doi :10.1038/ncomms1934
  • Fujii T, Iwane AH, Yanagida T, Namba K.
    Direct visualization of secondary structures of F-actin by electron cryomicroscopy.
    Nature 467(7316). 724-728 (2010) doi :10.1038/nature09372
  • Nishikawa S, Arimoto I, Ikezaki K, et al.
    Switch between Large Hand-Over-Hand and Small Inchworm-like Steps in Myosin VI.
    Cell 142(6). 879-888 (2010) doi :10.1016/j.cell.2010.08.033
  • Iwaki M, Iwane AH, Shimokawa T, et al.
    Brownian search-and-catch mechanism for myosin-VI steps.
    Nature Chemical Biology 5(6). 403-405 (2009) doi :10.1038/nchembio.171
  • Inomata K, Ohno A, Tochio H, et al.
    High-resolution multi-dimensional NMR spectroscopy of proteins in human cells.
    Nature 458(7234). 106-109 (2009) doi :10.1038/nature07839
  • Funatsu T, Harada Y, Tokunaga M, et al.
    Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous-solution.
    Nature 374(6522). 555-559 (1995) doi :10.1038/374555a0

All Publications